


After the Order

by Wundersmidget



Category: Star Wars - All Media Types, Star Wars: Rebels, Star Wars: The Clone Wars (2008) - All Media Types
Genre: Clones, F/M, Order 66, POV CT-7567 | Rex, Post-Order 66, Post-Star Wars: Return of the Jedi, Post-Star Wars: The Empire Strikes Back, Rebellion, References to Star Wars: The Clone Wars (2008), Star Wars: The Clone Wars (2008) Spoilers
Language: English
Status: Completed
Published: 2020-02-26
Updated: 2020-03-18
Packaged: 2021-02-28 00:54:15
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 7
Words: 4,282
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/22905037
Author URL: https://archiveofourown.org/users/Wundersmidget/pseuds/Wundersmidget
Summary: After the Clone Wars, CT-7567, better known as Captain Rex joined the Rebellion. But what happened to other Clones? We know that some stayed in the Empire, while others retired, often becoming mercenaries and Bounty Hunters, but what did they think? How did they feel? Lets find out.
Relationships: Boil & Numa (Star Wars), CC-1010 | Fox & CT-7567 | Rex, CC-2224 | Cody & CT-7567 | Rex, CC-5052 | Bly & CT-7567 | Rex, CT-7567 | Rex & Boil, CT-7567 | Rex & CC-4477 | Thire, CT-7567 | Rex & CC-8826 | Neyo, CT-7567 | Rex & Doom, CT-7567 | Rex/Ahsoka Tano, Dogma (Star Wars) & CT-7567 | Rex
Comments: 3
Kudos: 53





	1. The Commander and the Mercenary

**Author's Note:**

> Hey Everyone! So I can't promise how often this will be updated, or it's chapter count, I have the next two chapters completed and one on the way however so expect those over the next few days.
> 
> Take care, enjoy.
> 
> Wundersmidget

**\--3 ABY--**

Rex sat back in his quarters, it had only been a few weeks since he found himself assigned to the Millenium Falcon, he had been quite surprised, he was an old soldier, yet he found himself on the Rebellions best ship in the fleet.

He smirked, he had some idea of why he was on here however, Skywalker, it had not escaped High Command’s attention that he shared a surname of a well known Jedi, Rex’s Jedi. It was no coincidence, a General Skywalker’s son happily listened to Rex’s tales from the Clone Wars. Though there was something off, a sadness and depth that he hadn’t seen in his commander, not even around the Senator.

Rex knew of the relationship, communicating with armour on had made him a master in reading body language. He looked at one of the few things on his desk, it was a picture off the holonet, he had downloaded it years beforehand, the photo had been from one of the propaganda articles during the war, it was of him, Cody, Echo and Fives, it was the last time that they had all been together. Echo had gone missing, and before they had discovered that he was alive, Fives was dead. Now it was just Rex.

His Comlink sounded, it was the Princess.

“Captain, you’re needed in the cockpit, it’s urgent.”

Getting up he grabbed his helmet and put it on as he ran through the ship, best to be prepared after all.

Once there he saw why he was needed, they were coming up on the Home One, capital ship of the Rebellion. It was a short minutes wait until he felt the all-too familiar feeling of touchdown. The crew was quick in leaving the ship, apparently it was important that they get to the bridge immediately. Once there Rex saw a busy room, everyone talking at once, but once they saw him it all went silent.

“Captain Rex, we need you’re help.”

Heading to the command table Rex saw the problem. There was a number, but no ordinary number, this was quite clearly a Clone Trooper Identification number. CT-7567, his number.

“Patch them in.”

What Rex heard over the communicator made him step back in shock, it was a Clone’s voice.

“Captain Rex, is that you?”

Rex paused. Deciding to see what they wanted he responded.

“Yes, who is this? Who are you working for.”

“Ringo Vinda.”

Rex blinked.

“Doom?”

“That’s the one, I took youre advice, I’m chip free.”

Letting out a sigh of relief Rex nodded to the Admiral.

“He’s friendly.”

“Do I have permission to land?”

Ackbar nodded.

“We are opening a hangar bay door now, I will send Rex with a team to meet you once you have landed.”

“Understood, ETA 2 Minutes.”

2 minutes later, Rex was standing in the hangar, watching as a Consular Class cruiser, one of the ships that preceded the Clone Troopers land. Once the door opened he got his first look at a Commander Doom in over 20 years.

He, like Rex was still wearing the same armour that he had worn every day in the war, a few knicks and scratches were in it, and the green paint was a bit worn, but other than that it was pretty much the same.

“Hey Rex! Still fighting the good fight I see!”

Rex grinned.

“Believe it or not, I’m even working for a Skywalker!”

Doom indicated towards the ship.

“I have a surprise for you.”

Underneath his helmet Rex’s face took on a look of confusion, what could possibly have that was so special.

Doom pointed to where a few beings of assorted races, presumably who Doom had been hanging out with in the last 20 or so years escorted a single prisoner out of the craft. Even without the armour Rex would have recognised him a mile off.

Commander Fox.

He had obviously stayed in the service of the Empire, his hair was still cut to uniform length and he was clean shaven.

“I figured that you might want to deal with him yourself.”

Rex looked at the prisoner, this was the man who had killed Fives, caused so many deaths, the end of the Jedi. He smirked.

“Do you wanna talk?”

Rex and Doom went to the mess hall, grabbing a plate each they sat across from each other, Helmets off.

“You’ve done quite well for yourself Rex, you’re a part of the Rebellion.”

Rex grinned.

“I guess that when it comes down to it, I’m a soldier, all my life we were raised for war, for three years we were in the thick of it. Christophsis, Mandalore, Geonosis, and then we were declared defunct, replaced by civilians, some of us killed Jedi. I couldn’t sit back and watch the galaxy I was supposed to protect be melted down by the Empire. It feels good to be needed again.”

Doom nodded.

“You know, I would be glad to have you on my team, I do Bounty hunting know, no imperial contracts, just odd jobs for the scum and villainy in the universe, it’s really quite profitable, I think that Clone Force 99 is doing the same thing.”

Rex shook his head.

“As I said, I’m needed here, thanks for getting Fox for me, he will be of great use to the Rebellion, and to me as well.”

Doom nodded.

“I don’t think there's a clone out there without beef with Fox, why Thorn wasn’t commander I will never know.”

Rex nodded. 

“See you around, I have to get back to my crew.”

Rex nodded. He chucked at comlink towards Doom.

“If you ever are in trouble with the Empire, or you need a chat, I’ll be at the other end.”

Doom nodded.

“Take care Rex.”

“You too, see you around.”


	2. The Patient Clone

**Summary for the Chapter:**

> Rex attacks an Imperial Prison, but the commander seems rather familiar...

Rex entered the compound, they had it on good authority that a large number of Imperial Senators who had voiced sympathies with the Rebellion, especially after they themselves lost their seats alongside the rest of the Senate, were being held here for trial. Rex was the one assigned the task of 'releasing' them.

As his team entered the base they quickly neutralised the four guards at the entrance, splitting off into three groups, one to guard the entrance from counter-attack, another to liberate the prisoners, and the final team to capture the command post. As the team darted through the halls, taking the occasional stormtrooper out, Rex noted the increasing lack of security. Once they reached the entrance to the command room, the entire base obviously knew of their arrival, after a few moments they were able to eliminate the guards to the room and they ran inside. 

Rex assessed the room, there were 5 officers, 4 Stormtroopers - now deceased - Of the five officers however, one of these officers looked familiar.

It didn’t take Rex long to figure out why.

He had served with this face for years in the war, this face had died beside him, fought beside him, he had shared everything with this face.

For this face was that of a Clone trooper.

The clone obviously recognized him, like always, Rex was wearing his old clone armour. The officers eyes blazed in anger at him.

“Traitor!”

A short fistfight ensued, neither Clone able to get the upper hand, in the end Rex was able to slam his head into the wall and and held him against it.

“What's your name!”

The clone only spat in his face, Rex took out his pistol, holding it against the Clone’s head he asked again.

With no other option the clone answered.

“Commander Thire, Coruscant Guard.”

Rex had heard of Thire, if only in passing, he had apparently helped negotiate aid from Toydoria as a Lieutenant in the early days of the war, by the end of the war he was a commander, however failing to locate the body of Master Yoda after Order 66, he had reportedly even commanded the Emperor’s personal security detail for a while in the aftermath of the Jedi Purge.

Rex’s comlink went off. It was the prison team.

“Sir, the prisoners have been liberated, our transport is incoming now.”   
  


Indicating for his team to grab the other four officers he grabbed Thire’s arms, taking them through the prison they arrived at the entrance to the prison. True to their world a transport was waiting outside for his team. On board was a small team of soldiers who took the five prisoners into custody.

One they were back onboard the command ship Rex watched Thire be escorted away. Two clone commanders in a short amount of time, that gave Rex an idea.

A few hours later Rex left the command room. A new mission at hand. He had asked for permission in leading a small Alliance fleet to hunt down clones still serving the Empire. The reason for this, he had argued, was that due to bot superior training, and their experience in warfare, this made them high priority targets. One of the ships he had been given was a prison ship. Both Commander Thire and Commander Thorn were being transferred to it immediately. He had also been granted permission to capture any Imperial ships he felt necessary. Basically, he had been given a blank check, and he intended to see it to it’s full potential.


	3. Resistance on Ryloth

**Summary for the Chapter:**

> Boil had come far, climbed the Imperial rank structure, but it wasn't the same.

**Notes for the Chapter:**

> Hey everyone!
> 
> So I am taking suggestions for clones to do in future chapters, comment below who you think Rex should meet next.

Ryloth was a tough planet to keep in check, with Cham Syndulla’s rebels, and the support of the Rebellion, all forces on the planet certainly had their hands full.

Nor many more so than Captain Boil, after the war he had slowly climbed the ranks until he had been addressed his own region to control.

Of course, it wasn’t easy, he happened to have been given an area with a large amount of rebel activity, and the stormtroopers under his command were nowhere near the skill he and his brothers displayed in the war.

Suddenly the trooper beside him fell, a blaster burn in his back, turning around he found him and his men surrounded by Twi’leks. Stepping between them Boil recognized the face of Cham Syndulla, and Captain Rex.

Rex didn’t seem surprised to see him. 

Boil sighed, they were outnumbered, outgunned and outmatched.

“Lay down your weapons.”

As he and his stormtroopers lay their weapons down, Rex’s forces moved forwards, grabbing the stormtrooper’s weapons and slowly separating Boil from his team.

Once the Stormtrooper’s were far enough away from their commander, Rex stepped forward, grabbing Boil’s arms, Boil felt the feeling of Binders being placed on his hands. As he was led away Boil hung his head, but he knew better than to try to take on Rex, he was a legend among Clones for a reason.

As he was lead onto a transport, Rex watched the Ryloth Rebels lead the stormtroopers away, they would turn up at an Imperial camp, without armour or weapons, and sheepishly report to the camp commander that they lost the entire region’s commander.

As the ship took off, a Twi’lek walked into the room, Numa.

She looked exactly like he thought she would, a blaster pistol was strapped to her waist, what appeared to be stormtrooper armour adorned one arm.

She didn’t say a word as she sat on the floor across from him, but her mageta eyes bore into him, into his soul.

For 20 minutes they just sat there, neither moving their eyes, Boil had often thought of finding Numa, however he couldn’t bring himself to do it, he didn’t think she would be proud of him, obviously she wasn’t.

Boil had been on Utapau when Order 66 was issued, he hadn’t killed any Jedi himself, but he saw the AT-TE fire upon General Kenobi. He remembered the grim satisfaction that he felt as he saw the General’s mount fall into the pit below. 

A feeling of dread and guilt built up in his stomach.

What if they were wrong? Why would General Kenobi, any Jedi betray them?

Waxer had died because of Pong Krell, but Boil knew that he was the exception, not the norm. He had been in the room when Cody delivered the news of Krell’s treachery to the General, the horror and shock on the Jedi’s face was enough to know that this was no Jedi plot.

As the shuttle landed Numa got up, as she turned, Boil got a look at the writing on her armour.

“Boil”

As he was lead away a single tear rolled down the old soldier’s cheek.

Maybe, just maybe, the Jedi had been in the right.


	4. The Forgotten Prisoner

**Summary for the Chapter:**

> Dogma's day was meant to be like every other day that had preceeded this one, for over 20 years he had been in prison after all, but today was no normal day.

Dogma sighed as he paced his cell, over 24 years, far longer than he had spent in the war, even in training at Kamino, and this cell had been his for all of it. He was at the Imperial military prison on Coruscant. He had never even been given a trial, a chance to explain himself. He had heard of the traitorous acts committed by the Jedi, yet none had gone past his cell, the only Jedi that could even possibly be here was Barriss Offee, the Jedi traitor who had framed Commander Tano for her crimes.

She was probably long gone, legends of Inquisitors, fallen Jedi serving the Emperor had even reached Dogma’s ears, he wouldn’t be surprised if that traitor was one of them. 

Suddenly alarm bells sounded throughout the prison, in the distance, Dogma heard the familiar sound of explosions and Blaster fire, moments later, swarms of Rebellion soldiers ran into the complex, most ran into the detention wing where Rebellion P.O.Ws were held, however, one team ran into his cell block. And Dogma would recognize it’s leader a mile away.

“Rex?”

As Rex’s team came closer and surrounded his cell, Rex came right up to the wall separating the two.

“Dogma.”

“Rex.”

"How would you like to escape?"

"And fight against the Empire!? Are you mad!"

Rex's expression grew serious.

"Dogma, you of all people should know that good soldiers do not necessarily follow orders."

Dogma paused, images of the carnage on Umbara flew into his mind, his brothers ripped to shreds by a man they trusted, that he trusted, how Dogma had blindly followed these orders to the letter, even willing to order the death of his brothers to do so. But Krell had been a Jedi, but so had General Skywalker, and Commander Tano, General Kenobi too. He had blindly taken the words of his superior as law before, he had to be a fool to do so again.

Reluctantly nodding, Dogma stepped back, out of habit more than anything else, as Rex disabled the cell door. And as they rushed to the transports, Imperial security in hot pursuit until they reached hyperspace, Dogma waited to start work, a free soldier.


	5. Among the Stars

**Summary for the Chapter:**

> Bly's job is to extract the captured clones from the Rebellion.
> 
> That gets a bit complicated.

Bly never left a mission unfinished, if there ever was one it would be a stain on his spotless record, a stain he would do his damnedest to remove.

This mission was going to be no different.

The Empire had not failed to notice that an increasing number of clones in service of the Empire had been captured by the Rebellion, and while, at least in the mind of Bly, some, Fox, we're better off dead, it still fell to Bly to orchestrate their extraction.

After Order 66, he had been given what had basically replaced his regiment, this new unit was known as the Imperial Campaign Forces, slowly, over 20 years, he had seen his brothers leave, die, retire, and be replaced by recruits, they were never the standard he had come to expect from his men, they even tried to undermine his command, thinking that they were superior because he had been made in a tube, those that didn't apply for transfer were soon shown their place in the ranks of the ICF.

Unfortunately for Bly, this clone trooper prison was not a based on the ground, easier for his forces to capture, instead, the prison was based on a Nebulon B Frigate, under the command of Bly’s old friend, Captain Rex. 

Bly couldn’t comprehend why Rex would betray the Empire, nor side with the Jedi, after news of Rex’s apparent death on Mandalore, Bly, alongside Cody and Doom and Appo, alongside the 501st had mourned the loss of Rex, so many Clones had come to pay their respects at his makeshift funeral,, even Lord Vader himself had paid his respects. 

And then, 14 years later, they learnt that he was not just alive, but a traitor, it made Bly’s blood boil, Cody had been broken, the news of his old friend’s treachery contributing to his hated deployment on Kamino.

As his Star destroyer dropped out of Hyperspace, Bly saw the other members of his fleet dropping out, the interdictor vessel stopping the enemy’s retreat, as his shuttle flew down to the opponent's main hangar, surrounding TIE fighters drawing enemy fire away, Bly’s team waited in the hold. 

The door opened, Bly’s team ran off the ramp and into the hangar, losing two but taking out the forces defending the hangar. Running through, taking out Rebel forces on the way, Bly saw as some of his forces fell, his brothers wouldn’t have fallen. 

Finally Bly saw his target. Rex.

Rex turned to face him, his aged armour making Bly wish for his armour, not the armour of a stormtrooper, but his old, clone armour. 

A fierce duel followed, both masters in combat, their standoff quickly devolved into a hand to hand combat as both realised that blaster fire would get them nowhere, Bly felt Rex’s fit collide with his nose, blood flying everywhere as Bly’s knee collided with Rex’s chest, exchanging blows for ages, when suddenly, Bly felt his whole body freeze. Not out of fear or any physical condition.

But from something, different.

Bly saw a second being step into his sights as Rex grabbed his pistols.

The Togruta, as Bly quickly realised the lifeform was, turned to face him. 

Bly recognized that face, she was meant to be dead, but then, so was Rex, she was a traitor, Bly wanted to move, to run at her, end her traitorous life once and for all, but suddenly, an image flashed in his mind, a Twi'lek woman, face down on the Felucian ground, as he and his troopers fired into her body. He felt his body crumple as the Force released him, hitting the ground, only one thought went through his head.

_What had he done?_


	6. Brutal Stratagem

**Summary for the Chapter:**

> Rex makes a strike on Endor.

Neyo despised Endor, the trees that were so easily to lose yourself in if you weren’t careful, the tiny Ewoks that killed so many of his men.

But it was mainly the Rebellion that he hated.

He saw the flashes of light in the sky, up in space he knew that a mighty trap had been set, and they had received word that it had been sprung, of course, Neyo had his own problems.

A Rebellion force, 3 squads had raided his bunker, causing a fierce firefight to emerge, he was losing, Stormtroopers were not Clone Troopers.

Neyo didn’t care about the troopers dying around him, he hadn’t even cared when it was his brothers, why would he care now? 

He felt the familiar feel of a blaster pistol against the back of his helmet.

“Don’t move.”

He knew that voice, it was the same voice he had, but this one belonged to a traitor.

There was no fistfight, no blows exchanged, it would have been pointless anyway, Neyo was at a complete disadvantage.

As the unknown clone led him away, Neyo saw the last of his forces fall or surrender, Neyo didn’t care, they had failed.

A blast went off above him, looking up he saw the impossible. The Death Star was no more, and with it was his Emperor, Lord Vader, gone.

Neyo resisted his arrest, he must avenge the Emperor! But it was no use, he had failed.

Around him the Rebellion forces erupted into cheers, and the voice behind him spoke again.

“It’s funny, for three years we fought for a Republic that even now, doesn’t recognize clones as humans, instead of freedom, the Empire killed the Jedi and waged war on anyone who disagreed, and you know what Neyo, you liked it, you liked throwing away lives, even when it was your brothers, that’s why I never let you command the 501st.”

_ Rex. _

Neyo scowled underneath his helmet.

“The Empire brought order to the galaxy!”

“Order through fear.”

“Why would you fight us! The Empire fought for peace!”

“Because peace through the threat of destruction is no peace at all.”

Neyo stopped arguing, it was obvious that Rex was long gone, he made no sense now, hope was just a concept, only through strength would order ever prevail.

Neyo didn’t talk all the way up to the celebrating Rebel fleet, nor did he talk to his cellmate, Bly, Bly was too busy staring at the wall anyway.

Neyo would not talk, not in trial, not in prison, he would never betray his Emperor.

Not until the day he died.

Those would be his final orders.


	7. Reunited

Cody hated his assignment, he hated his troopers, he hated Kamino, the Kaminoans and most of all he hated the Rebellion.

He was meant to be getting new orders soon, apparently a contingency had been set off with the Emperor’s death, Cody didn’t know what this contingency was but he looked forward to an end to the endless drills and patrols he had to do in the terrible Kaminoan rain.

A blast went off a little way off from him, looking up he saw a fleet of Rebellion starships dropping out of Hyperspace, swarms of fighters and transports flying towards the city, yelling to his squad to start moving to defensive positions he radioed into the city control tower, ordering them to put the planet on high alert.

As enemy transports started landing, TIE Fighters and Interceptors flew in, distracting the ships starfighter escorts and taking out many transports, however for every transport destroyed, three more landed. A massive firefight took place, Rebellion and Imperial forces going at each other head on there was a beauty in it, one transport, an old Republic Gunship, bearing blue markings landed near him, as soon as the doors opened Rebellion forces ran out, firing at his forces, Cody fired into the attacking forces, two, three, four fell before they could get out the way, his standard issue blaster unleashing hell into the attacking forces. Around him his forces gained a foothold, standing against the attacking forces. In the distance, Cody saw an abandoned cloning facility drop beneath the waves. More transports landed around them, surrounding the Stormtroopers holding against the Rebel advance.

Beside him, two more Stormtroopers fell, Cody kicked some crates over in front of him, giving him a little bit of a shielded position. 

As three more of his forces fell, Cody was reduced to 7 men.

A grenade went off nearby, killing one trooper immediately and throwing another into the waves below. 5 left.

Two more were shot as they avoided a falling pylon. Three troopers left, surrounded on all sides.

The trooper to his left screamed as his arm was removed from its socket by an angry Wookie, throwing the body to the side the it advanced on Cody, the Wookie was only stopped by a well aimed blaster shot.

It was just him and one other stormtrooper remaining, a lucky shot hit his final ally in the face, ending his life immediately.

Cody held out against the forces all around him. Two, three, four more fell to his blaster. 

His left shoulder was hit, the right struck immediately after, sending him onto his back, unable to move his arms from the pain. As he lay, looking up at the Kaminoan sky, a helmet came into his vision. 

The traitor to the Empire, the one who had helped the Jedi, the one who had been a Rebel.

“Rex.”

Rex removed his helmet, unlike Cody, Rex was not clean shaven, he had allowed his beard to grow out, but unlike Cody, Rex still used his Clone Armour. 

“Umbara, Chrystophsis, Geonosis, we did all that together.”

“We could have served the Empire together.”

Rex grimaced.

“I would never betray the Jedi, never kill any of them, especially not Ashoka.”

Cody snarled.

“So you did have a thing for her,” He laughed. “Pity for you, the Jedi don’t allow attachments, remember?”

Rex smirked.

“Good thing she isn’t a Jedi then aye?”

Cody’s eyes widened.

“You’re dating a traitor!”

“The only traitor around here is you.”

Rex stepped back, we were the greatest of friends once Cody, brothers, but you betrayed the Jedi, I didn’t, you spent 20 long years on Kamino, meanwhile I got to have the time of my life, travelling the galaxy, fighting for a cause, and yes, dating a Jedi.”

Two Rebellion members came forward, loading Cody onto a stretcher and escorting him onto a transport. The last thing Cody saw before he fell unconscious was Rex, helmet back on, commanding the attack.

  
  


As the small Rebellion fleet sat in the NaJehda sector, a lone edi interceptor, dating back to the Clone Wars landed in a small hangar bay on the capital ship. As Ashoka Tano landed, she caught sight of her partner, Rex.

After she landed the two clutched each other in a tight embrace. A short moment later they broke apart.

Ashoka looked down, she had to tell him.

Rex sensed the change in demeanor. His eyes softened.

“Rex, I need to tell you something.” Ashoka began.

Rex nodded, after a pause Ashoka spoke.

“I’m pregnant.”


End file.
